Good practices in research

contributing to open science









Disclaimer

A paradigm shift


  • People used to think that it was ok not to disclose every step of our work, including data and code

  • An advantage

A paradigm shift

  • required by funding and journals (open science)
  • allows verification of the work (more rigorous, more reliable)
  • useful for your collaborators and yourself
  • increases visibility of the work (and citations)
  • fosters credibility and confidence in the scientific process
  • speeds up the scientific process

What does it mean?

Articles

Articles










A published article is just the tip of the iceberg that is the research process…




“An article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code and data, that produced the result.”

Claerbout and Karrenbach 1992.



The concepts

Wilson et al. 2016. Plos Comp Biol. https://arxiv.org/pdf/1609.00037.pdf

  • 1. Project Organization : File organisation

  • 2. Data management

  • 3. Software : Code structure & analysis flow

  • 4. Tracking Changes : version management

  • 5. Manuscripts

1. Project Organization


“Organizing the digital artifacts of a project to ease discovery and understanding.”




= Research compendium

1. Project Organization

1. Project Organization

2. Data management


  • Saving both raw and intermediate forms
  • Documenting all steps: code data acquisition process when possible, any transformation of the data is coded (and the transformed data seen as a result)
  • Creating tidy data amenable to analysis

2. Data management: Tidy data

3. Software


Writing, organizing, and sharing scripts and programs used in an analysis.

  • Respect code conventions from your community, https://style.tidyverse.org/

  • Document your code

  • Document the workflow (what is done in what order with what)

  • Document software used (OS, versions of R, versions of functions)

4. Tracking Changes


  • Track the evolution of your project

  • Use a version control software (Git).

5. Manuscripts


Writing manuscripts in a way that leaves an audit trail and minimizes manual merging of conflict.

LaTeX (e.g. overleaf)

Markdown

Quarto (https://quarto.org)

5. Manuscripts

Reproducible research?



data

code

documentation (e.g. article)

Reproducible research



Reproducible research